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Russell C, Campion M, Grove ME, Matsuda K, Klein TE, Ashley E, Naik H, Wheeler MT, Scott SA. Knowledge and attitudes on implementing cardiovascular pharmacogenomic testing. Clin Transl Sci 2024; 17:e13737. [PMID: 38421234 PMCID: PMC10903329 DOI: 10.1111/cts.13737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Pharmacogenomics has the potential to inform drug dosing and selection, reduce adverse events, and improve medication efficacy; however, provider knowledge of pharmacogenomic testing varies across provider types and specialties. Given that many actionable pharmacogenomic genes are implicated in cardiovascular medication response variability, this study aimed to evaluate cardiology providers' knowledge and attitudes on implementing clinical pharmacogenomic testing. Sixty-one providers responded to an online survey, including pharmacists (46%), physicians (31%), genetic counselors (15%), and nurses (8%). Most respondents (94%) reported previous genetics education; however, only 52% felt their genetics education prepared them to order a clinical pharmacogenomic test. In addition, most respondents (66%) were familiar with pharmacogenomics, with genetic counselors being most likely to be familiar (p < 0.001). Only 15% of respondents had previously ordered a clinical pharmacogenomic test and a total of 36% indicated they are likely to order a pharmacogenomic test in the future; however, the vast majority of respondents (89%) were interested in pharmacogenomic testing being incorporated into diagnostic cardiovascular genetic tests. Moreover, 84% of providers preferred pharmacogenomic panel testing compared to 16% who preferred single gene testing. Half of the providers reported being comfortable discussing pharmacogenomic results with their patients, but the majority (60%) expressed discomfort with the logistics of test ordering. Reported barriers to implementation included uncertainty about the clinical utility and difficulty choosing an appropriate test. Taken together, cardiology providers have moderate familiarity with pharmacogenomics and limited experience with test ordering; however, they are interested in incorporating pharmacogenomics into diagnostic genetic tests and ordering pharmacogenomic panels.
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Affiliation(s)
- Callan Russell
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
- Present address:
Northside HospitalAtlantaGeorgiaUSA
| | - MaryAnn Campion
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Megan E. Grove
- Clinical Genomics LaboratoryStanford MedicinePalo AltoCaliforniaUSA
- Present address:
Color HealthBurlingameCaliforniaUSA
| | - Kelly Matsuda
- Division of Pharmacy and CardiologyStanford Health CarePalo AltoCaliforniaUSA
| | - Teri E. Klein
- Department of Biomedical Data ScienceStanford UniversityStanfordCaliforniaUSA
| | - Euan Ashley
- Stanford Center for Inherited Cardiovascular DiseaseStanfordCaliforniaUSA
- Department of Medicine, Division of Cardiovascular MedicineStanford UniversityStanfordCaliforniaUSA
| | - Hetanshi Naik
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Matthew T. Wheeler
- Stanford Center for Inherited Cardiovascular DiseaseStanfordCaliforniaUSA
- Department of Medicine, Division of Cardiovascular MedicineStanford UniversityStanfordCaliforniaUSA
| | - Stuart A. Scott
- Clinical Genomics LaboratoryStanford MedicinePalo AltoCaliforniaUSA
- Department of PathologyStanford UniversityStanfordCaliforniaUSA
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Jain S, Bakolitsa C, Brenner SE, Radivojac P, Moult J, Repo S, Hoskins RA, Andreoletti G, Barsky D, Chellapan A, Chu H, Dabbiru N, Kollipara NK, Ly M, Neumann AJ, Pal LR, Odell E, Pandey G, Peters-Petrulewicz RC, Srinivasan R, Yee SF, Yeleswarapu SJ, Zuhl M, Adebali O, Patra A, Beer MA, Hosur R, Peng J, Bernard BM, Berry M, Dong S, Boyle AP, Adhikari A, Chen J, Hu Z, Wang R, Wang Y, Miller M, Wang Y, Bromberg Y, Turina P, Capriotti E, Han JJ, Ozturk K, Carter H, Babbi G, Bovo S, Di Lena P, Martelli PL, Savojardo C, Casadio R, Cline MS, De Baets G, Bonache S, Díez O, Gutiérrez-Enríquez S, Fernández A, Montalban G, Ootes L, Özkan S, Padilla N, Riera C, De la Cruz X, Diekhans M, Huwe PJ, Wei Q, Xu Q, Dunbrack RL, Gotea V, Elnitski L, Margolin G, Fariselli P, Kulakovskiy IV, Makeev VJ, Penzar DD, Vorontsov IE, Favorov AV, Forman JR, Hasenahuer M, Fornasari MS, Parisi G, Avsec Z, Çelik MH, Nguyen TYD, Gagneur J, Shi FY, Edwards MD, Guo Y, Tian K, Zeng H, Gifford DK, Göke J, Zaucha J, Gough J, Ritchie GRS, Frankish A, Mudge JM, Harrow J, Young EL, Yu Y, Huff CD, Murakami K, Nagai Y, Imanishi T, Mungall CJ, Jacobsen JOB, Kim D, Jeong CS, Jones DT, Li MJ, Guthrie VB, Bhattacharya R, Chen YC, Douville C, Fan J, Kim D, Masica D, Niknafs N, Sengupta S, Tokheim C, Turner TN, Yeo HTG, Karchin R, Shin S, Welch R, Keles S, Li Y, Kellis M, Corbi-Verge C, Strokach AV, Kim PM, Klein TE, Mohan R, Sinnott-Armstrong NA, Wainberg M, Kundaje A, Gonzaludo N, Mak ACY, Chhibber A, Lam HYK, Dahary D, Fishilevich S, Lancet D, Lee I, Bachman B, Katsonis P, Lua RC, Wilson SJ, Lichtarge O, Bhat RR, Sundaram L, Viswanath V, Bellazzi R, Nicora G, Rizzo E, Limongelli I, Mezlini AM, Chang R, Kim S, Lai C, O’Connor R, Topper S, van den Akker J, Zhou AY, Zimmer AD, Mishne G, Bergquist TR, Breese MR, Guerrero RF, Jiang Y, Kiga N, Li B, Mort M, Pagel KA, Pejaver V, Stamboulian MH, Thusberg J, Mooney SD, Teerakulkittipong N, Cao C, Kundu K, Yin Y, Yu CH, Kleyman M, Lin CF, Stackpole M, Mount SM, Eraslan G, Mueller NS, Naito T, Rao AR, Azaria JR, Brodie A, Ofran Y, Garg A, Pal D, Hawkins-Hooker A, Kenlay H, Reid J, Mucaki EJ, Rogan PK, Schwarz JM, Searls DB, Lee GR, Seok C, Krämer A, Shah S, Huang CV, Kirsch JF, Shatsky M, Cao Y, Chen H, Karimi M, Moronfoye O, Sun Y, Shen Y, Shigeta R, Ford CT, Nodzak C, Uppal A, Shi X, Joseph T, Kotte S, Rana S, Rao A, Saipradeep VG, Sivadasan N, Sunderam U, Stanke M, Su A, Adzhubey I, Jordan DM, Sunyaev S, Rousseau F, Schymkowitz J, Van Durme J, Tavtigian SV, Carraro M, Giollo M, Tosatto SCE, Adato O, Carmel L, Cohen NE, Fenesh T, Holtzer T, Juven-Gershon T, Unger R, Niroula A, Olatubosun A, Väliaho J, Yang Y, Vihinen M, Wahl ME, Chang B, Chong KC, Hu I, Sun R, Wu WKK, Xia X, Zee BC, Wang MH, Wang M, Wu C, Lu Y, Chen K, Yang Y, Yates CM, Kreimer A, Yan Z, Yosef N, Zhao H, Wei Z, Yao Z, Zhou F, Folkman L, Zhou Y, Daneshjou R, Altman RB, Inoue F, Ahituv N, Arkin AP, Lovisa F, Bonvini P, Bowdin S, Gianni S, Mantuano E, Minicozzi V, Novak L, Pasquo A, Pastore A, Petrosino M, Puglisi R, Toto A, Veneziano L, Chiaraluce R, Ball MP, Bobe JR, Church GM, Consalvi V, Cooper DN, Buckley BA, Sheridan MB, Cutting GR, Scaini MC, Cygan KJ, Fredericks AM, Glidden DT, Neil C, Rhine CL, Fairbrother WG, Alontaga AY, Fenton AW, Matreyek KA, Starita LM, Fowler DM, Löscher BS, Franke A, Adamson SI, Graveley BR, Gray JW, Malloy MJ, Kane JP, Kousi M, Katsanis N, Schubach M, Kircher M, Mak ACY, Tang PLF, Kwok PY, Lathrop RH, Clark WT, Yu GK, LeBowitz JH, Benedicenti F, Bettella E, Bigoni S, Cesca F, Mammi I, Marino-Buslje C, Milani D, Peron A, Polli R, Sartori S, Stanzial F, Toldo I, Turolla L, Aspromonte MC, Bellini M, Leonardi E, Liu X, Marshall C, McCombie WR, Elefanti L, Menin C, Meyn MS, Murgia A, Nadeau KCY, Neuhausen SL, Nussbaum RL, Pirooznia M, Potash JB, Dimster-Denk DF, Rine JD, Sanford JR, Snyder M, Cote AG, Sun S, Verby MW, Weile J, Roth FP, Tewhey R, Sabeti PC, Campagna J, Refaat MM, Wojciak J, Grubb S, Schmitt N, Shendure J, Spurdle AB, Stavropoulos DJ, Walton NA, Zandi PP, Ziv E, Burke W, Chen F, Carr LR, Martinez S, Paik J, Harris-Wai J, Yarborough M, Fullerton SM, Koenig BA, McInnes G, Shigaki D, Chandonia JM, Furutsuki M, Kasak L, Yu C, Chen R, Friedberg I, Getz GA, Cong Q, Kinch LN, Zhang J, Grishin NV, Voskanian A, Kann MG, Tran E, Ioannidis NM, Hunter JM, Udani R, Cai B, Morgan AA, Sokolov A, Stuart JM, Minervini G, Monzon AM, Batzoglou S, Butte AJ, Greenblatt MS, Hart RK, Hernandez R, Hubbard TJP, Kahn S, O’Donnell-Luria A, Ng PC, Shon J, Veltman J, Zook JM. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 2024; 25:53. [PMID: 38389099 PMCID: PMC10882881 DOI: 10.1186/s13059-023-03113-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/17/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
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Yang G, Alarcon C, Chanfreau C, Lee NH, Friedman P, Nutescu E, Tuck M, O'Brien T, Gong L, Klein TE, Chang KM, Tsao PS, Meltzer DO, Tuteja S, Perera MA. Investigation of genomic and transcriptomic risk factors in clopidogrel response in African Americans. medRxiv 2023:2023.12.05.23299140. [PMID: 38106031 PMCID: PMC10723512 DOI: 10.1101/2023.12.05.23299140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clopidogrel, an anti-platelet drug, used to prevent thrombosis after percutaneous coronary intervention. Clopidogrel resistance results in recurring ischemic episodes, with African Americans suffering disproportionately. The aim of this study was to identify biomarkers of clopidogrel resistance in African American patients. We conducted a genome-wide association study, including local ancestry adjustment, in 141 African Americans on clopidogrel to identify associations with high on-treatment platelet reactivity (HTPR). We validated genome-wide and suggestive hits in an independent cohort of African American clopidogrel patients (N = 823) from the Million Veteran's Program (MVP) along with in vitro functional follow up. We performed differential gene expression (DGE) analysis in whole blood with functional follow-up in MEG-01 cells. We identified rs7807369, within thrombospondin 7A (THSD7A), as significantly associated with increasing risk of HTPR (p = 4.56 × 10-9). Higher THSD7A expression was associated with HTPR in an independent gene expression cohort of clopidogrel treated patients (p = 0.004) and supported by increased gene expression on THSD7A in primary human endothelial cells carrying the risk haplotype. Two SNPs (rs1149515 and rs191786) were validated in the MVP cohort. DGE analysis identified an association with decreased LAIR1 expression to HTPR. LAIR1 knockdown in a MEG-01 cells resulted in increased expression of SYK and AKT1, suggesting an inhibitory role of LAIR1 in the Glycoprotein VI pathway. Notably, the CYP2C19 variants showed no association with clopidogrel response in the discovery or MVP cohorts. In summary, these finding suggest that other variants outside of CYP2C19 star alleles play an important role in clopidogrel response in African Americans.
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Affiliation(s)
- Guang Yang
- Department of Pharmacology, Center for Pharmacogenomics, Fienberg School of Medicine, Northwestern University, Chicago IL
| | - Cristina Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Fienberg School of Medicine, Northwestern University, Chicago IL
| | | | - Norman H Lee
- Department of Pharmacology and Physiology, George Washington University, 2300 I Street NW, Washington, DC, 20037, USA
| | - Paula Friedman
- Department of Pharmacology, Center for Pharmacogenomics, Fienberg School of Medicine, Northwestern University, Chicago IL
| | - Edith Nutescu
- Department of Pharmacy Practice and Center for Pharmacoepidemiology and Pharmacoeconomic Research, University of Illinois Chicago, College of Pharmacy, Chicago, IL
| | - Matthew Tuck
- Washington DC VA Medical Center, Washington, DC and The George Washington University, Washington, DC
| | - Travis O'Brien
- Department of Pharmacology and Physiology, George Washington University, 2300 I Street NW, Washington, DC, 20037, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Philip S Tsao
- VA Palo Alto Healthcare System and Stanford University, Palo Alto, CA
| | - David O Meltzer
- Section of Hospital Medicine, Department of Medicine, University of Chicago, Chicago, IL
| | - Sony Tuteja
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Fienberg School of Medicine, Northwestern University, Chicago IL
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Turner AJ, Nofziger C, Ramey BE, Ly RC, Bousman CA, Agúndez JAG, Sangkuhl K, Whirl-Carrillo M, Vanoni S, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Moyer AM, Gaedigk A. PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting. Clin Pharmacol Ther 2023; 114:1220-1237. [PMID: 37669183 PMCID: PMC10840842 DOI: 10.1002/cpt.3044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.
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Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | | | | | - Reynold C Ly
- Department of Medical and Molecular Genetics, Division of Diagnostic Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chad A Bousman
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - José AG Agúndez
- University of Extremadura, Cáceres, Spain
- Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Gualberto Ruano
- Institute of Living, Hartford Hospital (Hartford CT) and Department of Psychiatry, University of Connecticut School of Medicine (Farmington CT), USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Houda Hachad, Department of Clinical Operations, AccessDx Laboratories, Houston, Texas, USA
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Ann M Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrea Gaedigk
- Children’s Mercy Research Institute (CMRI), Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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Gonzalez-Suarez AD, Thorn CF, Whirl-Carrillo M, Klein TE. PharmGKB summary: disulfiram pathway. Pharmacogenet Genomics 2023; 33:207-216. [PMID: 37728645 PMCID: PMC10627108 DOI: 10.1097/fpc.0000000000000509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Affiliation(s)
| | | | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
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Li B, Sangkuhl K, Whaley R, Woon M, Keat K, Whirl-Carrillo M, Ritchie MD, Klein TE. Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank. Am J Hum Genet 2023; 110:1628-1647. [PMID: 37757824 PMCID: PMC10577080 DOI: 10.1016/j.ajhg.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads to an underestimation of certain alleles. We applied the Pharmacogenomics Clinical Annotation Tool (PharmCAT) on an integrated 200K UK Biobank genetic dataset (N = 200,044). Based on PharmCAT results, we estimated PGx frequencies (alleles, diplotypes, phenotypes, and activity scores) for 17 pharmacogenes in five biogeographic groups: European, Central/South Asian, East Asian, Afro-Caribbean, and Sub-Saharan African. PGx frequencies were distinct for each biogeographic group. Even biogeographic groups with similar proportions of phenotypes were driven by different sets of dominant PGx alleles. PharmCAT also identified "no-function" alleles that were rare or seldom tested in certain groups by previous studies, e.g., SLCO1B1∗31 in the Afro-Caribbean (3.0%) and Sub-Saharan African (3.9%) groups. Estimated PGx frequencies are disseminated via the PharmGKB (The Pharmacogenomics Knowledgebase: www.pharmgkb.org). We demonstrate that genetic biobanks such as the UK Biobank are a robust resource for estimating PGx frequencies. Improving our understanding of PGx allele and phenotype frequencies provides guidance for future PGx studies and clinical genetic test panel design, and better serves individuals from wider biogeographic backgrounds.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ryan Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Karl Keat
- Genomics and Computational Biology PhD Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Medicine (BMIR), Stanford University, Stanford, CA 94305, USA.
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Williams S, Ligas C, Oloff L, Klein TE. The Role of Epigenomics in Mapping Potential Precursors for Foot and Ankle Tendinopathy: A Systematic Review. Foot Ankle Spec 2023; 16:446-454. [PMID: 37165881 DOI: 10.1177/19386400231170967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Tendinopathy of the foot and ankle is a common clinical problem for which the exact etiology is poorly understood. The field of epigenetics has been a recent focus of this investigation. The purpose of this article was to review the genomic advances in foot and ankle tendinopathy that could potentially be used to stratify disease risk and create preventative or therapeutic agents. A multi-database search of PubMed, Cochrane, Google Scholar, and clinicaltrials.gov from January 1, 2000 to July 1, 2022 was performed. A total of 18 articles met inclusion and exclusion criteria for this review. The majority of such research utilized case-control candidate gene association to identify different genetic risk factors associated with chronic tendinopathy. Polymorphisms in collagen genes COL5A1, COL27A1, and COL1A1 were noted at a significantly higher frequency in Achilles tendinopathy versus control groups. Other allelic variations that were observed at an increased incidence in Achilles tendinopathy were TNC and CASP8. The extracellular matrix (ECM) demonstrated macroscopic changes in Achilles tendinopathy, including an increase in aggrecan and biglycan mRNA expression, and increased expression of multiple matrix metalloproteinases. Cytokine expression was also influenced in pathology and aberrantly demonstrated dynamic response to mechanical load. The pathologic accumulation of ECM proteins and cytokine expression alters the adaptive response normal tendon has to physiologic stress, further propagating the risk for tendinopathy. By identifying and understanding the epigenetic mediators that lead to tendinopathy, therapeutic agents can be developed to target the exact underlying etiology and minimize side effects.Level of Evidence: Level IV: Systematic Review of Level II-IV Studies.
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Affiliation(s)
- Samantha Williams
- Department of Podiatric Surgery, Silicon Valley Reconstructive Foot and Ankle Fellowship, Palo Alto Medical Foundation, Mountain View, California
| | - Chandler Ligas
- Department of Podiatric Surgery, Silicon Valley Reconstructive Foot and Ankle Fellowship, Palo Alto Medical Foundation, Mountain View, California
| | - Lawrence Oloff
- Department of Podiatric Surgery, Silicon Valley Reconstructive Foot and Ankle Fellowship, Palo Alto Medical Foundation, Mountain View, California
- St. Mary's Medical Center, San Francisco, California
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine, Stanford Center for Biomedical Informatics Research (BMIR), and Stanford University, Stanford, California
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Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, Klein TE, Richards CS, Stewart DR, Martin CL. ACMG SF v3.2 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100866. [PMID: 37347242 PMCID: PMC10524344 DOI: 10.1016/j.gim.2023.100866] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/23/2023] Open
Abstract
Clinicians are encouraged to document the reasons for the use of a particular procedure or test, whether or not it is in conformance with this statement. Clinicians also are advised to take notice of the date this statement was adopted, and to consider other medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures. Where individual authors are listed, the views expressed may not reflect those of authors’ employers or affiliated institutions.
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Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Noura S Abul-Husn
- Department of Medicine, Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe, Inc., Sunnyvale, CA
| | | | - Kyle Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Michael H Gollob
- Division of Cardiology, Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Adam S Gordon
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine, Stanford University, Stanford, CA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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9
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Bousman CA, Stevenson JM, Ramsey LB, Sangkuhl K, Kevin Hicks J, Strawn JR, Singh AB, Ruaño G, Mueller DJ, Tsermpini EE, Brown JT, Bell GC, Steven Leeder J, Gaedigk A, Scott SA, Klein TE, Caudle KE, Bishop JR. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6, CYP2C19, CYP2B6, SLC6A4, and HTR2A Genotypes and Serotonin Reuptake Inhibitor Antidepressants. Clin Pharmacol Ther 2023; 114:51-68. [PMID: 37032427 PMCID: PMC10564324 DOI: 10.1002/cpt.2903] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
Serotonin reuptake inhibitor antidepressants, including selective serotonin reuptake inhibitors (SSRIs; i.e., citalopram, escitalopram, fluoxetine, fluvoxamine, paroxetine, and sertraline), serotonin and norepinephrine reuptake inhibitors (i.e., desvenlafaxine, duloxetine, levomilnacipran, milnacipran, and venlafaxine), and serotonin modulators with SSRI-like properties (i.e., vilazodone and vortioxetine) are primary pharmacologic treatments for major depressive and anxiety disorders. Genetic variation in CYP2D6, CYP2C19, and CYP2B6 influences the metabolism of many of these antidepressants, which may potentially affect dosing, efficacy, and tolerability. In addition, the pharmacodynamic genes SLC6A4 (serotonin transporter) and HTR2A (serotonin-2A receptor) have been examined in relation to efficacy and side effect profiles of these drugs. This guideline updates and expands the 2015 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 and CYP2C19 genotypes and SSRI dosing and summarizes the impact of CYP2D6, CYP2C19, CYP2B6, SLC6A4, and HTR2A genotypes on antidepressant dosing, efficacy, and tolerability. We provide recommendations for using CYP2D6, CYP2C19, and CYP2B6 genotype results to help inform prescribing these antidepressants and describe the existing data for SLC6A4 and HTR2A, which do not support their clinical use in antidepressant prescribing.
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Affiliation(s)
- Chad A. Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, and Community Health Sciences, University of Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Alberta, Canada
- Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - James M. Stevenson
- Departments of Medicine and Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura B. Ramsey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Kevin Hicks
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL, USA
| | - Jeffrey R. Strawn
- Department of Psychiatry & Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
- Divisions of Child & Adolescent Psychiatry and Clinical Pharmacology Cincinnati, Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Ajeet B. Singh
- School of Medicine, IMPACT Institute, Deakin University, Australia
| | - Gualberto Ruaño
- Institute of Living at Hartford Hospital, Hartford, CT, USA
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Daniel J. Mueller
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Ontario, Canada
| | - Evangelia Eirini Tsermpini
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jacob T. Brown
- Department of Pharmacy Practice & Pharmaceutical Sciences, University of Minnesota College of Pharmacy, Duluth, MN, USA
| | | | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stuart A. Scott
- Department of Pathology, Stanford University, Palo Alto, CA, USA
- Stanford Medicine Clinical Genomics Program, Stanford Medicine, Stanford, CA, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jeffrey R. Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN, USA
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10
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Gammal RS, Pirmohamed M, Somogyi AA, Morris SA, Formea CM, Elchynski AL, Oshikoya KA, McLeod HL, Haidar CE, Whirl-Carrillo M, Klein TE, Caudle KE, Relling MV. Expanded Clinical Pharmacogenetics Implementation Consortium Guideline for Medication Use in the Context of G6PD Genotype. Clin Pharmacol Ther 2023; 113:973-985. [PMID: 36049896 PMCID: PMC10281211 DOI: 10.1002/cpt.2735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with development of acute hemolytic anemia in the setting of oxidative stress, which can be caused by medication exposure. Regulatory agencies worldwide warn against the use of certain medications in persons with G6PD deficiency, but in many cases, this information is conflicting, and the clinical evidence is sparse. This guideline provides information on using G6PD genotype as part of the diagnosis of G6PD deficiency and classifies medications that have been previously implicated as unsafe in individuals with G6PD deficiency by one or more sources. We classify these medications as high, medium, or low to no risk based on a systematic review of the published evidence of the gene-drug associations and regulatory warnings. In patients with G6PD deficiency, high-risk medications should be avoided, medium-risk medications should be used with caution, and low-to-no risk medications can be used with standard precautions, without regard to G6PD phenotype. This new document replaces the prior Clinical Pharmacogenetics Implementation Consortium guideline for rasburicase therapy in the context of G6PD genotype (updates at: www.cpicpgx.org).
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Affiliation(s)
- Roseann S. Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Munir Pirmohamed
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew A. Somogyi
- Discipline of Pharmacology, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Sarah A. Morris
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Cancer Pharmacology and Pharmacogenomics, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Christine M. Formea
- Department of Pharmacy and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT, USA
| | | | - Kazeem A. Oshikoya
- Department of Pharmacology, Therapeutics and Toxicology, College of Medicine, Lagos State University, Ikeja, Lagos, Nigeria
| | - Howard L. McLeod
- Intermountain Precision Genomics, Intermountain Healthcare, St George, UT, USA
| | - Cyrine E. Haidar
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mary V. Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
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11
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Li B, Sangkuhl K, Keat K, Whaley RM, Woon M, Verma S, Dudek S, Tuteja S, Verma A, Whirl-Carrillo M, Ritchie MD, Klein TE. How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2023; 113:1036-1047. [PMID: 36350094 PMCID: PMC10121724 DOI: 10.1002/cpt.2790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022]
Abstract
Pharmacogenomics (PGx) investigates the genetic influence on drug response and is an integral part of precision medicine. While PGx testing is becoming more common in clinical practice and may be reimbursed by Medicare/Medicaid and commercial insurance, interpreting PGx testing results for clinical decision support is still a challenge. The Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been designed to tackle the need for transparent, automatic interpretations of patient genetic data. PharmCAT incorporates a patient's genotypes, annotates PGx information (allele, genotype, and phenotype), and generates a report with PGx guideline recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and/or the Dutch Pharmacogenetics Working Group (DPWG). PharmCAT has introduced new features in the last 2 years, including a variant call format (VCF) Preprocessor, the inclusion of DPWG guidelines, and functionalities for PGx research. For example, researchers can use the VCF Preprocessor to prepare biobank-scale data for PharmCAT. In addition, PharmCAT enables the assessment of novel partial and combination alleles that are composed of known PGx variants and can call CYP2D6 genotypes based on single and deletions in the input VCF file. This tutorial provides materials and detailed step-by-step instructions for how to use PharmCAT in a versatile way that can be tailored to users' individual needs.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karl Keat
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan M. Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, PA, USA
| | - Scott Dudek
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sony Tuteja
- Department of Medicine, University of Pennsylvania, PA, USA
| | - Anurag Verma
- Department of Medicine, University of Pennsylvania, PA, USA
| | | | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Medicine (BMIR), Stanford University, Stanford, CA, USA
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12
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Ramsey LB, Gong L, Lee SB, Wagner JB, Zhou X, Sangkuhl K, Adams SM, Straka RJ, Empey PE, Boone EC, Klein TE, Niemi M, Gaedigk A. PharmVar GeneFocus: SLCO1B1. Clin Pharmacol Ther 2023; 113:782-793. [PMID: 35797228 PMCID: PMC10900141 DOI: 10.1002/cpt.2705] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 11/06/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) is now providing star (*) allele nomenclature for the highly polymorphic human SLCO1B1 gene encoding the organic anion transporting polypeptide 1B1 (OATP1B1) drug transporter. Genetic variation within the SLCO1B1 gene locus impacts drug transport, which can lead to altered pharmacokinetic profiles of several commonly prescribed drugs. Variable OATP1B1 function is of particular importance regarding hepatic uptake of statins and the risk of statin-associated musculoskeletal symptoms. To introduce this important drug transporter gene into the PharmVar database and serve as a unified reference of haplotype variation moving forward, an international group of gene experts has performed an extensive review of all published SLCO1B1 star alleles. Previously published star alleles were self-assigned by authors and only loosely followed the star nomenclature system that was first developed for cytochrome P450 genes. This nomenclature system has been standardized by PharmVar and is now applied to other important pharmacogenes such as SLCO1B1. In addition, data from the 1000 Genomes Project and investigator-submitted data were utilized to confirm existing haplotypes, fill knowledge gaps, and/or define novel star alleles. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by the Clinical Pharmacogenetics Implementation Consortium (CPIC) 2022 guideline on statin-associated musculoskeletal symptoms.
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Affiliation(s)
- Laura B Ramsey
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Seung-Been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Korea
| | - Jonathan B Wagner
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Solomon M Adams
- School of Pharmacy, Shenandoah University, Fairfax, Virginia, USA
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Philip E Empey
- School of Pharmacy and Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Mikko Niemi
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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13
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Rodriguez-Antona C, Savieo JL, Lauschke VM, Sangkuhl K, Drögemöller BI, Wang D, van Schaik RHN, Gilep AA, Peter AP, Boone EC, Ramey BE, Klein TE, Whirl-Carrillo M, Pratt VM, Gaedigk A. PharmVar GeneFocus: CYP3A5. Clin Pharmacol Ther 2022; 112:1159-1171. [PMID: 35202484 PMCID: PMC9399309 DOI: 10.1002/cpt.2563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 01/31/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP3A5 gene. Genetic variation within the CYP3A5 gene locus impacts the metabolism of several clinically important drugs, including the immunosuppressants tacrolimus, sirolimus, cyclosporine, and the benzodiazepine midazolam. Variable CYP3A5 activity is of clinical importance regarding tacrolimus metabolism. This GeneFocus provides a CYP3A5 gene summary with a focus on aspects regarding standardized nomenclature. In addition, this review also summarizes recent changes and updates, including the retirement of several allelic variants and provides an overview of how PharmVar CYP3A5 star allele nomenclature is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
- Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, USA
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Arul P Peter
- Coriell Life Sciences, Philadelphia, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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14
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Verma SS, Keat K, Li B, Hoffecker G, Risman M, Sangkuhl K, Whirl-Carrillo M, Dudek S, Verma A, Klein TE, Ritchie MD, Tuteja S. Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population. J Transl Med 2022; 20:550. [PMID: 36443877 PMCID: PMC9703665 DOI: 10.1186/s12967-022-03745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/30/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pharmacogenomics (PGx) aims to utilize a patient's genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for 24 genes that affect 72 medications. Despite strong evidence linking PGx alleles to drug response, there is a large gap in the implementation and return of actionable pharmacogenetic findings to patients in standard clinical practice. In this study, we evaluated opportunities for genetically guided medication prescribing in a diverse health system and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population. METHODS A retrospective analysis of the Penn Medicine electronic health records (EHRs), which includes ~ 3.3 million patients between 2012 and 2020, provides a snapshot of the trends in prescriptions for drugs with genotype-based prescribing guidelines ('CPIC level A or B') in the Penn Medicine health system. The Penn Medicine BioBank (PMBB) consists of a diverse group of 43,359 participants whose EHRs are linked to genome-wide SNP array and whole exome sequencing (WES) data. We used the Pharmacogenomics Clinical Annotation Tool (PharmCAT), to annotate PGx alleles from PMBB variant call format (VCF) files and identify samples with actionable PGx alleles. RESULTS We identified ~ 316.000 unique patients that were prescribed at least 2 drugs with CPIC Level A or B guidelines. Genetic analysis in PMBB identified that 98.9% of participants carry one or more PGx actionable alleles where treatment modification would be recommended. After linking the genetic data with prescription data from the EHR, 14.2% of participants (n = 6157) were prescribed medications that could be impacted by their genotype (as indicated by their PharmCAT report). For example, 856 participants received clopidogrel who carried CYP2C19 reduced function alleles, placing them at increased risk for major adverse cardiovascular events. When we stratified by genetic ancestry, we found disparities in PGx allele frequencies and clinical burden. Clopidogrel users of Asian ancestry in PMBB had significantly higher rates of CYP2C19 actionable alleles than European ancestry users of clopidrogrel (p < 0.0001, OR = 3.68). CONCLUSIONS Clinically actionable PGx alleles are highly prevalent in our health system and many patients were prescribed medications that could be affected by PGx alleles. These results illustrate the potential utility of preemptive genotyping for tailoring of medications and implementation of PGx into routine clinical care.
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Affiliation(s)
- Shefali S. Verma
- grid.25879.310000 0004 1936 8972Department of Pathology & Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Karl Keat
- grid.25879.310000 0004 1936 8972Genomics & Computational Biology PhD Program, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Binglan Li
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Glenda Hoffecker
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Marjorie Risman
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | | | - Katrin Sangkuhl
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Michelle Whirl-Carrillo
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Scott Dudek
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Anurag Verma
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Teri E. Klein
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, CA USA
| | - Marylyn D. Ritchie
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Sony Tuteja
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
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15
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Lee CR, Luzum JA, Sangkuhl K, Gammal RS, Sabatine MS, Stein CM, Kisor DF, Limdi NA, Lee YM, Scott SA, Hulot JS, Roden DM, Gaedigk A, Caudle KE, Klein TE, Johnson JA, Shuldiner AR. Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2C19 Genotype and Clopidogrel Therapy: 2022 Update. Clin Pharmacol Ther 2022; 112:959-967. [PMID: 35034351 PMCID: PMC9287492 DOI: 10.1002/cpt.2526] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/22/2021] [Indexed: 11/06/2022]
Abstract
CYP2C19 catalyzes the bioactivation of the antiplatelet prodrug clopidogrel, and CYP2C19 genotype impacts clopidogrel active metabolite formation. CYP2C19 intermediate and poor metabolizers who receive clopidogrel experience reduced platelet inhibition and increased risk for major adverse cardiovascular and cerebrovascular events. This guideline is an update to the 2013 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for the use of clopidogrel based on CYP2C19 genotype and includes expanded indications for CYP2C19 genotype-guided antiplatelet therapy, increased strength of recommendation for CYP2C19 intermediate metabolizers, updated CYP2C19 genotype to phenotype translation, and evidence from an expanded literature review (updates at www.cpicpgx.org).
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Affiliation(s)
- Craig R. Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Roseann S. Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marc S. Sabatine
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - C. Michael Stein
- Division of Clinical Pharmacology, Departments of Medicine and Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David F. Kisor
- Department of Pharmaceutical Sciences, Manchester University, Fort Wayne, IN, USA
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yee Ming Lee
- Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Stuart A. Scott
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Jean-Sébastien Hulot
- Université de Paris, CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, F-75015, Paris, France
| | - Dan M. Roden
- Departments of Medicine and Pharmacology, Office of Personalized Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Alan R. Shuldiner
- Department of Medicine, and Program for Genomic and Personalized Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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16
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Maillard M, Gong L, Nishii R, Yang JJ, Whirl-Carrillo M, Klein TE. PharmGKB summary: acyclovir/ganciclovir pathway. Pharmacogenet Genomics 2022; 32:201-208. [PMID: 35665708 PMCID: PMC9179945 DOI: 10.1097/fpc.0000000000000474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Maud Maillard
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Li Gong
- Departments of Biomedical Data Science
| | - Rina Nishii
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Teri E Klein
- Departments of Biomedical Data Science
- Medicine (BMIR), Stanford University, Stanford, California, USA
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17
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Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, Klein TE, Richards CS, Stewart DR, Martin CL. ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1407-1414. [DOI: 10.1016/j.gim.2022.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
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18
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Thomas A, Fang MC, Kogan S, Hubbard CC, Friedman PN, Gong L, Klein TE, Nutescu EA, O’Brien TJ, Tuck M, Perera MA, Schwartz JB. Apixaban Concentrations in Routine Clinical Care of Older Adults With Nonvalvular Atrial Fibrillation. JACC Adv 2022; 1:100039. [PMID: 37961076 PMCID: PMC10643025 DOI: 10.1016/j.jacadv.2022.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
BACKGROUND Direct-acting oral anticoagulants are first-line agents for prevention of stroke in patients with nonvalvular atrial fibrillation (NVAF), but data are limited for the oldest patients, and with reduced dosing. OBJECTIVES To determine steady-state apixaban peak and trough concentrations during routine care of older adults with NVAF, compare concentrations to clinical trial concentrations, and explore factors associated with concentrations. METHODS A cross-sectional study of medically stable older adults with NVAF (≥75 years or ≥70 years if Black) receiving apixaban. Peak (2-4.4 hours post-dose) and trough (before next dose) concentrations were determined by anti-Xa activity calibrated chromogenic assay. Patient characteristics associated with concentrations were determined by multivariate modeling. RESULTS The median age of patients (n = 115) was 80 (interquartile range: 77-84) years. The cohort comprised 46 women and 69 men; of which 98 are White, 11 Black, and 6 Asian. With 5 mg twice daily per labelling (n = 88), peak concentrations were higher in women: 248 ± 105 vs 174 ± 67 ng/mL in men (P < 0.001) and exceeded expected 95% range in 6 of 30 vs 0 of 55 men (P = 0.002). With 2.5 mg twice daily per label (n = 11), concentrations were <5 mg twice daily (peak: 136 ± 87 vs 201 ± 90 ng/mL, P = 0.026; trough: 65 ± 28 vs 109 ± 56 ng/mL, P < 0.001), but not different than 2.5 mg twice daily without reduction criteria (n = 13; peak: 132 ± 88; trough: 65 ± 31 ng/mL). Covariates associated with concentrations included sex, number of daily medications, and creatinine clearance. CONCLUSIONS Older women had higher than expected peak apixaban concentrations, and 2.5 mg twice daily produced lower concentrations than standard dosing. Factors not currently included in dosing recommendations affected concentrations. The impact of apixaban concentrations on outcomes needs evaluation.
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Affiliation(s)
- Alveena Thomas
- Division of Geriatrics, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Margaret C. Fang
- Division of Hospital Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Scott Kogan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Colin C. Hubbard
- Division of Hospital Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Paula N. Friedman
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Teri E. Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, California, USA
| | - Edith A. Nutescu
- Department of Pharmacy Practice and Center for Pharmacoepidemiology and Pharmacoeconomic Research, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Travis J. O’Brien
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Matthew Tuck
- Washington DC VA Medical Center, Washington, District of Columbia, USA
- Department of Medicine, The George Washington University, Washington, District of Columbia, USA
| | - Minoli A. Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Janice B. Schwartz
- Division of Geriatrics, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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19
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Miller E, Norwood C, Giles JB, Huddart R, Karnes JH, Whirl-Carrillo M, Klein TE. PharmGKB summary: heparin-induced thrombocytopenia pathway, adverse drug reaction. Pharmacogenet Genomics 2022; 32:117-124. [PMID: 35102073 PMCID: PMC8988468 DOI: 10.1097/fpc.0000000000000465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Elise Miller
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Charles Norwood
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Jason B. Giles
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Jason H. Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA
- Department of Biomedical Informatics Research, Stanford University, Stanford, CA
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20
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Tayeh MK, Gaedigk A, Goetz MP, Klein TE, Lyon E, McMillin GA, Rentas S, Shinawi M, Pratt VM, Scott SA. Clinical pharmacogenomic testing and reporting: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:759-768. [PMID: 35177334 DOI: 10.1016/j.gim.2021.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomic testing interrogates germline sequence variants implicated in interindividual drug response variability to infer a drug response phenotype and to guide medication management for certain drugs. Specifically, discrete aspects of pharmacokinetics, such as drug metabolism, and pharmacodynamics, as well as drug sensitivity, can be predicted by genes that code for proteins involved in these pathways. Pharmacogenomics is unique and differs from inherited disease genetics because the drug response phenotype can be drug-dependent and is often unrecognized until an unexpected drug reaction occurs or a patient fails to respond to a medication. Genes and variants with sufficiently high levels of evidence and consensus may be included in a clinical pharmacogenomic test; however, result interpretation and phenotype prediction can be challenging for some genes and medications. This document provides a resource for laboratories to develop and implement clinical pharmacogenomic testing by summarizing publicly available resources and detailing best practices for pharmacogenomic nomenclature, testing, result interpretation, and reporting.
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Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO; Department of Pediatrics, UMKC School of Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Matthew P Goetz
- Department of Pharmacology and Oncology, Mayo Clinic, Rochester, MN
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Elaine Lyon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Marwan Shinawi
- Division of Genetics & Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, CA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA
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21
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Cooper‐DeHoff RM, Niemi M, Ramsey LB, Luzum JA, Tarkiainen EK, Straka RJ, Gong L, Tuteja S, Wilke RA, Wadelius M, Larson EA, Roden DM, Klein TE, Yee SW, Krauss RM, Turner RM, Palaniappan L, Gaedigk A, Giacomini KM, Caudle KE, Voora D. The Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for
SLCO1B1, ABCG2
, and
CYP2C9
and statin‐associated musculoskeletal symptoms. Clin Pharmacol Ther 2022; 111:1007-1021. [PMID: 35152405 PMCID: PMC9035072 DOI: 10.1002/cpt.2557] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/02/2022] [Indexed: 11/09/2022]
Abstract
Statins reduce cholesterol, prevent cardiovascular disease, and are among the most commonly prescribed medications in the world. Statin-associated musculoskeletal symptoms (SAMS) impact statin adherence and ultimately can impede the long-term effectiveness of statin therapy. There are several identified pharmacogenetic variants that impact statin disposition and adverse events during statin therapy. SLCO1B1 encodes a transporter (SLCO1B1; alternative names include OATP1B1 or OATP-C) that facilitates the hepatic uptake of all statins. ABCG2 encodes an efflux transporter (BCRP) that modulates the absorption and disposition of rosuvastatin. CYP2C9 encodes a phase I drug metabolizing enzyme responsible for the oxidation of some statins. Genetic variation in each of these genes alters systemic exposure to statins (i.e., simvastatin, rosuvastatin, pravastatin, pitavastatin, atorvastatin, fluvastatin, lovastatin), which can increase the risk for SAMS. We summarize the literature supporting these associations and provide therapeutic recommendations for statins based on SLCO1B1, ABCG2, and CYP2C9 genotype with the goal of improving the overall safety, adherence, and effectiveness of statin therapy. This document replaces the 2012 and 2014 Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for SLCO1B1 and simvastatin-induced myopathy.
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Affiliation(s)
- Rhonda M. Cooper‐DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine College of Pharmacy University of Florida Gainesville Florida USA
- Division of Cardiovascular Medicine Department of Medicine College of Medicine University of Florida Gainesville Florida USA
| | - Mikko Niemi
- Department of Clinical Pharmacology Individualized Drug Therapy Research Program University of Helsinki Helsinki Finland
- HUS Diagnostic Center Helsinki University Hospital Helsinki Finland
- Individualized Drug Therapy Research Program University of Helsinki Helsinki Finland
| | - Laura B. Ramsey
- Divisions of Clinical Pharmacology & Research in Patient Services Cincinnati Children’s Hospital Medical Center Cincinnati OH USA
- Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy University of Michigan College of Pharmacy Ann Arbor
| | - E. Katriina Tarkiainen
- Department of Clinical Pharmacology Individualized Drug Therapy Research Program University of Helsinki Helsinki Finland
- HUS Diagnostic Center Helsinki University Hospital Helsinki Finland
- Individualized Drug Therapy Research Program University of Helsinki Helsinki Finland
| | - Robert J. Straka
- Department of Experimental and Clinical Pharmacology University of Minnesota College of Pharmacy Minneapolis Minnesota USA
| | - Li Gong
- Department of Biomedical Data Science School of Medicine Stanford University Stanford California USA
| | - Sony Tuteja
- Department of Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Russell A. Wilke
- Department of Internal Medicine University of South Dakota Sanford School of Medicine Sioux Falls South Dakota USA
| | - Mia Wadelius
- Department of Medical Sciences Clinical Pharmacogenomics & Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Eric A. Larson
- Department of Internal Medicine University of South Dakota Sanford School of Medicine Sioux Falls South Dakota USA
| | - Dan M. Roden
- Division of Cardiovascular Medicine and Division of Clinical Pharmacology Department of Medicine Vanderbilt University Medical Center Nashville TN USA
- Department of Pharmacology and Department of Biomedical Informatics Vanderbilt University Medical Center Nashville TN USA
| | - Teri E. Klein
- Department of Biomedical Data Science School of Medicine Stanford University Stanford California USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco California USA
| | - Ronald M. Krauss
- Departments of Pediatrics and Medicine University of California San Francisco CA USA
| | - Richard M. Turner
- The Wolfson Centre for Personalised Medicine University of Liverpool Liverpool UK
| | - Latha Palaniappan
- Division of Primary Care and Population Health Stanford University School of Medicine Stanford CA USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation Children's Mercy Kansas City and School of Medicine University of Missouri‐Kansas City Kansas City MO USA
| | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco California USA
| | - Kelly E. Caudle
- Division of Pharmaceutical Sciences Department of Pharmacy and Pharmaceutical Sciences St. Jude Children’s Research Hospital Memphis TN USA
| | - Deepak Voora
- Department of Medicine Duke Center for Applied Genomics & Precision Medicine Duke University School of Medicine Durham NC USA
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22
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McDermott JH, Wolf J, Hoshitsuki K, Huddart R, Caudle KE, Whirl-Carrillo M, Steyger PS, Smith RJH, Cody N, Rodriguez-Antona C, Klein TE, Newman WG. Clinical Pharmacogenetics Implementation Consortium Guideline for the Use of Aminoglycosides Based on MT-RNR1 Genotype. Clin Pharmacol Ther 2022; 111:366-372. [PMID: 34032273 PMCID: PMC8613315 DOI: 10.1002/cpt.2309] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 02/03/2023]
Abstract
Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity). MT-RNR1 is a gene that encodes the 12s rRNA subunit and is the mitochondrial homologue of the prokaryotic 16s rRNA. Some MT-RNR1 variants (i.e., m.1095T>C; m.1494C>T; m.1555A>G) more closely resemble the bacterial 16s rRNA subunit and result in increased risk of aminoglycoside-induced hearing loss. Use of aminoglycosides should be avoided in individuals with an MT-RNR1 variant associated with an increased risk of aminoglycoside-induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for the use of aminoglycosides based on MT-RNR1 genotype (updates at https://cpicpgx.org/guidelines/ and www.pharmgkb.org).
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Affiliation(s)
- John Henry McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Peter S. Steyger
- Translational Hearing Center, Biomedical Sciences, Creighton University, National Center for Rehabilitative Auditory Research, VA Portland Health Care System, Portland, Oregon, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Internal Medicine (Nephrology), Pediatrics and Molecular Physiology & Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Neal Cody
- Department of Genetics and Genomic Sciences, Ichan School of Medicine at Mount Sinai, New York, New York, USA,Sema4, Stamford, Connecticut, USA
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA,Department of Medicine, Stanford University, Stanford, California, USA
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK,Correspondence: William Newman ()
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23
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Abstract
The Pharmacogenomics Knowledgebase (PharmGKB) is an integrated online knowledge resource for the understanding of how genetic variation contributes to variation in drug response. Our focus includes not only pharmacogenomic information useful for clinical implementation (e.g., drug dosing guidelines and annotated drug labels), but also information to catalyze scientific research and drug discovery (e.g., variant-drug annotations and drug-centered pathways). As of April 2021, the annotated content of PharmGKB spans 715 drugs, 1761 genes, 227 diseases, 165 clinical guidelines, and 784 drug labels. We have manually curated data from more than 9000 published papers to generate the content of PharmGKB. Recently, we have also implemented an automated natural language processing (NLP) tool to broaden our coverage of the pharmacogenomic literature. This article contains a basic protocol describing how to navigate the PharmGKB website to retrieve information on how genes and genetic variations affect drug efficacy and toxicity. It also includes a protocol on how to use PharmGKB to facilitate interpretation of findings for a pharmacogenomic variant genotype or metabolizer phenotype. PharmGKB is freely available at http://www.pharmgkb.org. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Navigating the homepage of PharmGKB and searching by drug Basic Protocol 2: Using PharmGKB to facilitate interpretation of pharmacogenomic variant genotypes or metabolizer phenotypes.
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Affiliation(s)
- Li Gong
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
| | - Michelle Whirl-Carrillo
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
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24
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Miller DT, Lee K, Chung WK, Gordon AS, Herman GE, Klein TE, Stewart DR, Amendola LM, Adelman K, Bale SJ, Gollob MH, Harrison SM, Hershberger RE, McKelvey K, Richards CS, Vlangos CN, Watson MS, Martin CL. Correction to: ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1582-1584. [PMID: 34345026 PMCID: PMC10764012 DOI: 10.1038/s41436-021-01278-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Adam S Gordon
- Department of Pharmacology & Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail E Herman
- Professor Emeritus, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Teri E Klein
- Departments of Biomedical Data Science & Medicine, Stanford University, Stanford, CA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | | | - Michael H Gollob
- Division of Cardiology and Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kent McKelvey
- Departments of Genetics and Family Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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25
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Whirl-Carrillo M, Huddart R, Gong L, Sangkuhl K, Thorn CF, Whaley R, Klein TE. An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine. Clin Pharmacol Ther 2021; 110:563-572. [PMID: 34216021 PMCID: PMC8457105 DOI: 10.1002/cpt.2350] [Citation(s) in RCA: 243] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022]
Abstract
Clinical annotations are one of the most popular resources available on the Pharmacogenomics Knowledgebase (PharmGKB). Each clinical annotation summarizes the association between variant‐drug pairs, shows relevant findings from the curated literature, and is assigned a level of evidence (LOE) to indicate the strength of support for that association. Evidence from the pharmacogenomic literature is curated into PharmGKB as variant annotations, which can be used to create new clinical annotations or added to existing clinical annotations. This means that the same clinical annotation can be worked on by multiple curators over time. As more evidence is curated into PharmGKB, the task of maintaining consistency when assessing all the available evidence and assigning an LOE becomes increasingly difficult. To remedy this, a scoring system has been developed to automate LOE assignment to clinical annotations. Variant annotations are scored according to certain attributes, including study size, reported P value, and whether the variant annotation supports or fails to find an association. Clinical guidelines or US Food and Drug Administration (FDA)‐approved drug labels which give variant‐specific prescribing guidance are also scored. The scores of all annotations attached to a clinical annotation are summed together to give a total score for the clinical annotation, which is used to calculate an LOE. Overall, the system increases transparency, consistency, and reproducibility in LOE assignment to clinical annotations. In combination with increased standardization of how clinical annotations are written, use of this scoring system helps to ensure that PharmGKB clinical annotations continue to be a robust source of pharmacogenomic information.
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Affiliation(s)
- Michelle Whirl-Carrillo
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Li Gong
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Caroline F Thorn
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Ryan Whaley
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Stanford, California, USA
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26
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Gaedigk A, Casey ST, Whirl-Carrillo M, Miller NA, Klein TE. Pharmacogene Variation Consortium: A Global Resource and Repository for Pharmacogene Variation. Clin Pharmacol Ther 2021; 110:542-545. [PMID: 34091888 DOI: 10.1002/cpt.2321] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, USA
| | - Scott T Casey
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
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27
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Sangkuhl K, Claudio-Campos K, Cavallari LH, Agundez JAG, Whirl-Carrillo M, Duconge J, Del Tredici AL, Wadelius M, Rodrigues Botton M, Woodahl EL, Scott SA, Klein TE, Pratt VM, Daly AK, Gaedigk A. PharmVar GeneFocus: CYP2C9. Clin Pharmacol Ther 2021; 110:662-676. [PMID: 34109627 DOI: 10.1002/cpt.2333] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Karla Claudio-Campos
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Jose A G Agundez
- University Institute of Molecular Pathology Biomarkers, University of Extremadura, Asthma, Adverse Drug Reactions and Allergy (ARADyAL) Institute de Salud Carlos III, Cáceres, Spain
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | | | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA.,Stanford Health Care Clinical Genomics Laboratory, Palo Alto, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, USA
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28
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Miller DT, Lee K, Chung WK, Gordon AS, Herman GE, Klein TE, Stewart DR, Amendola LM, Adelman K, Bale SJ, Gollob MH, Harrison SM, Hershberger RE, McKelvey K, Richards CS, Vlangos CN, Watson MS, Martin CL. ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1381-1390. [PMID: 34012068 DOI: 10.1038/s41436-021-01172-3] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/17/2023] Open
Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Adam S Gordon
- Department of Pharmacology & Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail E Herman
- Professor Emeritus, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Teri E Klein
- Departments of Biomedical Data Science & Medicine, Stanford University, Stanford, CA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | | | - Michael H Gollob
- Division of Cardiology and Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kent McKelvey
- Departments of Genetics and Family Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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29
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Desta Z, El-Boraie A, Gong L, Somogyi AA, Lauschke VM, Dandara C, Klein K, Miller NA, Klein TE, Tyndale RF, Whirl-Carrillo M, Gaedigk A. PharmVar GeneFocus: CYP2B6. Clin Pharmacol Ther 2021; 110:82-97. [PMID: 33448339 DOI: 10.1002/cpt.2166] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP2B6 gene. Genetic variation within the CYP2B6 gene locus impacts the metabolism or bioactivation of clinically important drugs. Of particular importance are efficacy and safety concerns regarding: efavirenz, which is used for the treatment of HIV type-1 infection; methadone, a mainstay in the treatment of opioid use disorder and as an analgesic; ketamine, used as an antidepressant and analgesic; and bupropion, which is prescribed to treat depression and for smoking cessation. This GeneFocus provides a comprehensive overview and summary of CYP2B6 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
- Zeruesenay Desta
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ahmed El-Boraie
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology & Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Neil A Miller
- Genomic Medicine Center, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Rachel F Tyndale
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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30
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Empey PE, Pratt VM, Hoffman JM, Caudle KE, Klein TE. Expanding evidence leads to new pharmacogenomics payer coverage. Genet Med 2021; 23:830-832. [PMID: 33627827 DOI: 10.1038/s41436-021-01117-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Philip E Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James M Hoffman
- Office of Quality & Patient Care, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Medicine, Stanford University, Stanford, CA, USA
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31
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Crews KR, Monte AA, Huddart R, Caudle KE, Kharasch ED, Gaedigk A, Dunnenberger HM, Leeder JS, Callaghan JT, Samer CF, Klein TE, Haidar CE, Van Driest SL, Ruano G, Sangkuhl K, Cavallari LH, Müller DJ, Prows CA, Nagy M, Somogyi AA, Skaar TC. Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6, OPRM1, and COMT Genotypes and Select Opioid Therapy. Clin Pharmacol Ther 2021; 110:888-896. [PMID: 33387367 DOI: 10.1002/cpt.2149] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
Abstract
Opioids are mainly used to treat both acute and chronic pain. Several opioids are metabolized to some extent by CYP2D6 (codeine, tramadol, hydrocodone, oxycodone, and methadone). Polymorphisms in CYP2D6 have been studied for an association with the clinical effect and safety of these drugs. Other genes that have been studied for their association with opioid clinical effect or adverse events include OPRM1 (mu receptor) and COMT (catechol-O-methyltransferase). This guideline updates and expands the 2014 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 genotype and codeine therapy and includes a summation of the evidence describing the impact of CYP2D6, OPRM1, and COMT on opioid analgesia and adverse events. We provide therapeutic recommendations for the use of CYP2D6 genotype results for prescribing codeine and tramadol and describe the limited and/or weak data for CYP2D6 and hydrocodone, oxycodone, and methadone, and for OPRM1 and COMT for clinical use.
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Affiliation(s)
- Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew A Monte
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Evan D Kharasch
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kanas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Henry M Dunnenberger
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kanas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - John T Callaghan
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Caroline Flora Samer
- Clinical Pharmacology and Toxicology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Cyrine E Haidar
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gualberto Ruano
- Institute of Living Hartford Hospital, Genomas Lab of Personalized Health, University of Connecticut School of Medicine and University of Puerto Rico Medical Sciences, Hartford, Connecticut, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Daniel J Müller
- Department of Psychiatry, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mohamed Nagy
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Todd C Skaar
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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32
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McInnes G, Lavertu A, Sangkuhl K, Klein TE, Whirl-Carrillo M, Altman RB. Pharmacogenetics at Scale: An Analysis of the UK Biobank. Clin Pharmacol Ther 2020; 109:1528-1537. [PMID: 33237584 DOI: 10.1002/cpt.2122] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/22/2020] [Indexed: 01/06/2023]
Abstract
Pharmacogenetics (PGx) studies the influence of genetic variation on drug response. Clinically actionable associations inform guidelines created by the Clinical Pharmacogenetics Implementation Consortium (CPIC), but the broad impact of genetic variation on entire populations is not well understood. We analyzed PGx allele and phenotype frequencies for 487,409 participants in the UK Biobank, the largest PGx study to date. For 14 CPIC pharmacogenes known to influence human drug response, we find that 99.5% of individuals may have an atypical response to at least 1 drug; on average they may have an atypical response to 10.3 drugs. Nearly 24% of participants have been prescribed a drug for which they are predicted to have an atypical response. Non-European populations carry a greater frequency of variants that are predicted to be functionally deleterious; many of these are not captured by current PGx allele definitions. Strategies for detecting and interpreting rare variation will be critical for enabling broad application of pharmacogenetics.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informfatics Training Program, Stanford University, Stanford, California, USA
| | - Adam Lavertu
- Biomedical Informfatics Training Program, Stanford University, Stanford, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, USA
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33
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Higgins J, Dalgleish R, den Dunnen JT, Barsh G, Freeman PJ, Cooper DN, Cullinan S, Davies KE, Dorkins H, Gong L, Imoto I, Klein TE, Korf B, Misra A, Paalman MH, Ratzel S, Reichardt JKV, Rehm HL, Tokunaga K, Weck KE, Cutting GR. Verifying nomenclature of DNA variants in submitted manuscripts: Guidance for journals. Hum Mutat 2020; 42:3-7. [PMID: 33252176 DOI: 10.1002/humu.24144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022]
Abstract
Documenting variation in our genomes is important for research and clinical care. Accuracy in the description of DNA variants is therefore essential. To address this issue, the Human Variome Project convened a committee to evaluate the feasibility of requiring authors to verify that all variants submitted for publication complied with a widely accepted standard for description. After a pilot study of two journals, the committee agreed that requiring authors to verify that variants complied with Human Genome Variation Society nomenclature is a reasonable step toward standardizing the worldwide inventory of human variation.
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Affiliation(s)
- Jan Higgins
- American College of Medical Genetics and Genomics, Bethesda, Maryland, USA
| | - Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Johan T den Dunnen
- Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Peter J Freeman
- Division of Informatics, Imaging & Data Science, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Sara Cullinan
- American Society of Human Genetics, Rockville, Maryland, USA
| | - Kay E Davies
- Department of Physiology, Anatomy and Genetics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Huw Dorkins
- St Peter's College, University of Oxford, Oxford, UK.,Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Issei Imoto
- Division of Molecular Genetics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Bruce Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Adya Misra
- Public Library of Science, San Francisco, California, USA.,Public Library of Science, Cambridge, UK
| | - Mark H Paalman
- Cell and Molecular Biology Research, Wiley Periodicals LLC, Hoboken, New Jersey, USA
| | - Sarah Ratzel
- American Society of Human Genetics, Rockville, Maryland, USA
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
| | - Heidi L Rehm
- Medical & Population Genetics Program and Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Katsushi Tokunaga
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics and Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Garry R Cutting
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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34
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Lewis JP, Backman JD, Reny JL, Bergmeijer TO, Mitchell BD, Ritchie MD, Déry JP, Pakyz RE, Gong L, Ryan K, Kim EY, Aradi D, Fernandez-Cadenas I, Lee MTM, Whaley RM, Montaner J, Gensini GF, Cleator JH, Chang K, Holmvang L, Hochholzer W, Roden DM, Winter S, Altman RB, Alexopoulos D, Kim HS, Gawaz M, Bliden KP, Valgimigli M, Marcucci R, Campo G, Schaeffeler E, Dridi NP, Wen MS, Shin JG, Fontana P, Giusti B, Geisler T, Kubo M, Trenk D, Siller-Matula JM, Ten Berg JM, Gurbel PA, Schwab M, Klein TE, Shuldiner AR. Pharmacogenomic polygenic response score predicts ischaemic events and cardiovascular mortality in clopidogrel-treated patients. Eur Heart J Cardiovasc Pharmacother 2020; 6:203-210. [PMID: 31504375 DOI: 10.1093/ehjcvp/pvz045] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/15/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023]
Abstract
AIMS Clopidogrel is prescribed for the prevention of atherothrombotic events. While investigations have identified genetic determinants of inter-individual variability in on-treatment platelet inhibition (e.g. CYP2C19*2), evidence that these variants have clinical utility to predict major adverse cardiovascular events (CVEs) remains controversial. METHODS AND RESULTS We assessed the impact of 31 candidate gene polymorphisms on adenosine diphosphate (ADP)-stimulated platelet reactivity in 3391 clopidogrel-treated coronary artery disease patients of the International Clopidogrel Pharmacogenomics Consortium (ICPC). The influence of these polymorphisms on CVEs was tested in 2134 ICPC patients (N = 129 events) in whom clinical event data were available. Several variants were associated with on-treatment ADP-stimulated platelet reactivity (CYP2C19*2, P = 8.8 × 10-54; CES1 G143E, P = 1.3 × 10-16; CYP2C19*17, P = 9.5 × 10-10; CYP2B6 1294 + 53 C > T, P = 3.0 × 10-4; CYP2B6 516 G > T, P = 1.0 × 10-3; CYP2C9*2, P = 1.2 × 10-3; and CYP2C9*3, P = 1.5 × 10-3). While no individual variant was associated with CVEs, generation of a pharmacogenomic polygenic response score (PgxRS) revealed that patients who carried a greater number of alleles that associated with increased on-treatment platelet reactivity were more likely to experience CVEs (β = 0.17, SE 0.06, P = 0.01) and cardiovascular-related death (β = 0.43, SE 0.16, P = 0.007). Patients who carried eight or more risk alleles were significantly more likely to experience CVEs [odds ratio (OR) = 1.78, 95% confidence interval (CI) 1.14-2.76, P = 0.01] and cardiovascular death (OR = 4.39, 95% CI 1.35-14.27, P = 0.01) compared to patients who carried six or fewer of these alleles. CONCLUSION Several polymorphisms impact clopidogrel response and PgxRS is a predictor of cardiovascular outcomes. Additional investigations that identify novel determinants of clopidogrel response and validating polygenic models may facilitate future precision medicine strategies.
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Affiliation(s)
- Joshua P Lewis
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Joshua D Backman
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Jean-Luc Reny
- Department of Internal Medicine, Béziers Hospital, 2 Rue Valentin Hau, BP 740, Béziers 34525, France.,Department of Medicine, Geneva Platelet Group, University of Geneva School of Medicine, University Hospitals of Geneva, 24 rue du Général-Dufour, Genève 4 CH-1211, Switzerland
| | - Thomas O Bergmeijer
- Department of Cardiology, Antonius Center for Platelet Function Research, St Antonius Hospital, P O Box 2500, Nieuwegein 3432 EM, The Netherlands
| | - Braxton D Mitchell
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, 10 N. Greene St., Baltimore, MD 21201, USA
| | - Marylyn D Ritchie
- Center for Translational Bioinformatics, Institute for Biomedical Informatics, University of Pennsylvania, A301 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Jean-Pierre Déry
- Quebec Heart and Lung Institute, University Laval, 2725 chemin Sainte-Foy, Quebec City G1V 4G5, Canada
| | - Ruth E Pakyz
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, 443 Via Ortega, Room 213, Stanford, CA 94305, USA
| | - Kathleen Ryan
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Eun-Young Kim
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Bokji-ro 75, Busangjin-gu, Busan 614-735, South Korea
| | - Daniel Aradi
- Department of Cardiology, Heart Center Balatonfüred, 2 Gyogy Ter, Balatonfured 8230, Hungary
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetic Group, Fundació Docencia i Recerca Mutuaterrassa, 508221 Terrassa, Barcelona 8041, Spain.,Department of Neurology, Vall d'Hebron Institute of Research, Passeig Vall d'Hebron, Barcelona 8035, Spain
| | - Ming Ta Michael Lee
- Genomic Medicine Institute, Geisinger Health System, 100 N. Academy Ave., Danville, PA 17822, USA
| | - Ryan M Whaley
- Department of Biomedical Data Science, Stanford University, 443 Via Ortega, Room 213, Stanford, CA 94305, USA
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Passeig Vall d'Hebron 119-129, Barcelona 8035, Spain
| | - Gian Franco Gensini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence 50055, Italy
| | - John H Cleator
- Division of Cardiology, Vanderbilt University Medical Center, 2215B Garland Avenue, Nashville, TN 37232, USA.,Department of Pharmacology, Vanderbilt University Medical Center, 2215B Garland Avenue, Nashville, TN 37232, USA
| | - Kiyuk Chang
- Department of Internal Medicine, Cardiology Division, Seoul St. Mary's Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul 6591, South Korea
| | - Lene Holmvang
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Inge Lehmannsvej 7 - 2142, Copenhagen 2100, Denmark
| | - Willibald Hochholzer
- Department of Cardiology and Angiology II, University Heart Center Freiburg, Suedring 15, Bad Krozingen 79189, Germany
| | - Dan M Roden
- Department of Pharmacology, Vanderbilt University Medical Center, 2215B Garland Avenue, Nashville, TN 37232, USA.,Department of Medicine, Vanderbilt University Medical Center, 2215B Garland Avenue, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, 2215B Garland Avenue, Nashville, TN 37232, USA
| | - Stefan Winter
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376 Germany
| | - Russ B Altman
- Department of Bioengineering, Genetics, and Medicine, Stanford University, 443 Via Ortega Drive, Shriram Room 209, Stanford, CA 94305, USA
| | | | - Ho-Sook Kim
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Gaegum2-dong 622-165, Busanjin-Gu, Busan 614-735, South Korea
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University of Tübingen, Otfired-Müller-Straße 10, Tübingen 72076, Germany
| | - Kevin P Bliden
- Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, 3300 Gallows Rd, Falls Church, VA 22042, USA
| | - Marco Valgimigli
- Department of Cardiology, Bern University Hospital, Freiburgstrasse 8, Bern 3010, Switzerland
| | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence 50055, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Largo G. Alessandro Brambilla, Florence 50134, Italy
| | - Gianluca Campo
- Department of Cardiology, University Hospital of Ferrara, Via Aldo Moro 8, Cona (FE), Ferrara 44123, Italy.,GVM Care & Research, Maria Cecilia Hospital, Via Madonna di Genova, 1, Cotignola 48033, Italy
| | - Elke Schaeffeler
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376 Germany
| | - Nadia P Dridi
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Inge Lehmannsvej 7 - 2142, Copenhagen 2100, Denmark
| | - Ming-Shien Wen
- Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and School of Medicine, Chang Gung University, No. 5, Fuxing St, Guishan Dist., Taoyuan City 333, Taiwan
| | - Jae Gook Shin
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Gaegum2-dong 622-165, Busanjin-Gu, Busan 614-735, South Korea
| | - Pierre Fontana
- Department of Medicine, Geneva Platelet Group, University of Geneva School of Medicine, University Hospitals of Geneva, 24 rue du Général-Dufour, Genève 4 CH-1211, Switzerland.,Division of Angiology and Haemostasis, University Hospitals of Geneva, 24 Rue Gabrielle-Perret-Gentil, Geneva 1205, Switzerland
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence 50055, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Largo G. Alessandro Brambilla, Florence 50134, Italy
| | - Tobias Geisler
- Department of Cardiology and Angiology, University of Tübingen, Otfired-Müller-Straße 10, Tübingen 72076, Germany
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Dietmar Trenk
- Department of Cardiology and Angiology II, Clinical Pharmacology, University Heart Centre Freiburg, Suedring 15, Bad Krozingen D-79189, Germany
| | - Jolanta M Siller-Matula
- Department of Cardiology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna 1090, Austria
| | - Jurriën M Ten Berg
- Department of Cardiology, Antonius Center for Platelet Function Research, St Antonius Hospital, P O Box 2500, Nieuwegein 3432 EM, The Netherlands
| | - Paul A Gurbel
- Department of Cardiology and Angiology, University of Tübingen, Otfired-Müller-Straße 10, Tübingen 72076, Germany
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376 Germany.,Department of Clinical Pharmacology, University of Tuebingen, Otfried-Mueller-Strasse 10, Tuebingen 72076, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Otfried-Mueller-Strasse 10, Tuebingen 72076, Germany
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, 443 Via Ortega, Room 213, Stanford, CA 94305, USA.,Department of Bioengineering, Genetics, and Medicine, Stanford University, 443 Via Ortega Drive, Shriram Room 209, Stanford, CA 94305, USA
| | - Alan R Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, 670 W. Baltimore St., Baltimore, MD 21201, USA
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35
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Bousman CA, Bengesser SA, Aitchison KJ, Amare AT, Aschauer H, Baune BT, Asl BB, Bishop JR, Burmeister M, Chaumette B, Chen LS, Cordner ZA, Deckert J, Degenhardt F, DeLisi LE, Folkersen L, Kennedy JL, Klein TE, McClay JL, McMahon FJ, Musil R, Saccone NL, Sangkuhl K, Stowe RM, Tan EC, Tiwari AK, Zai CC, Zai G, Zhang J, Gaedigk A, Müller DJ. Review and Consensus on Pharmacogenomic Testing in
Psychiatry. Pharmacopsychiatry 2020; 54:5-17. [DOI: 10.1055/a-1288-1061] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractThe implementation of pharmacogenomic (PGx) testing in psychiatry remains modest,
in part due to divergent perceptions of the quality and completeness of the
evidence base and diverse perspectives on the clinical utility of PGx testing
among psychiatrists and other healthcare providers. Recognizing the current lack
of consensus within the field, the International Society of Psychiatric Genetics
assembled a group of experts to conduct a narrative synthesis of the PGx
literature, prescribing guidelines, and product labels related to psychotropic
medications as well as the key considerations and limitations related to the use
of PGx testing in psychiatry. The group concluded that to inform medication
selection and dosing of several commonly-used antidepressant and antipsychotic
medications, current published evidence, prescribing guidelines, and product
labels support the use of PGx testing for 2 cytochrome P450 genes (CYP2D6,
CYP2C19). In addition, the evidence supports testing for human leukocyte
antigen genes when using the mood stabilizers carbamazepine (HLA-A and
HLA-B), oxcarbazepine (HLA-B), and phenytoin (CYP2C9, HLA-B). For
valproate, screening for variants in certain genes (POLG, OTC, CSP1) is
recommended when a mitochondrial disorder or a urea cycle disorder is suspected.
Although barriers to implementing PGx testing remain to be fully resolved, the
current trajectory of discovery and innovation in the field suggests these
barriers will be overcome and testing will become an important tool in
psychiatry.
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Affiliation(s)
- Chad A. Bousman
- Departments of Medical Genetics, Psychiatry, Physiology &
Pharmacology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of
Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB,
Canada
- Department of Psychiatry, Melbourne Medical School, The University of
Melbourne, Melbourne, VIC, Australia
| | - Susanne A. Bengesser
- Department of Psychiatry and Psychotherapeutic Medicine, Medical
University of Graz, Austria
| | - Katherine J. Aitchison
- Departments of Psychiatry, Medical Genetics and the Neuroscience and
Mental Health Institute, University of Alberta, Edmonton, AB,
Canada
| | - Azmeraw T. Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide,
Adelaide, SA, Australia
- South Australian Health and Medical Research Institute (SAHMRI),
Adelaide, SA, Australia
| | - Harald Aschauer
- Biopsychosocial Corporation (BioPsyC), non-profit association, Vienna,
Austria
| | - Bernhard T. Baune
- Department of Psychiatry and Psychotherapy, University of
Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of
Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University
of Melbourne, Parkville, VIC, Australia
| | - Bahareh Behroozi Asl
- Departments of Psychiatry, Medical Genetics and the Neuroscience and
Mental Health Institute, University of Alberta, Edmonton, AB,
Canada
| | - Jeffrey R. Bishop
- Department of Experimental and Clinical Pharmacology, University of
Minnesota College of Pharmacy and Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA
| | - Margit Burmeister
- Michigan Neuroscience Institute and Departments of Computational
Medicine & Bioinformatics, Human Genetics and Psychiatry, The University
of Michigan, Ann Arbor MI, USA
| | - Boris Chaumette
- Institute of Psychiatry and Neuroscience of Paris, GHU Paris
Psychiatrie & Neurosciences, University of Paris, Paris,
France
- Department of Psychiatry, McGill University, Montreal,
Canada
| | - Li-Shiun Chen
- Departments of Psychiatry and Genetics, Washington University School of
Medicine in St. Louis, USA
| | - Zachary A. Cordner
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins
University School of Medicine, Baltimore, MD, USA
| | - Jürgen Deckert
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of
Mental Health, Würzburg, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, School of Medicine
& University Hospital Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy, University Hospital Essen, University of Duisburg-Essen,
Duisburg, Germany
| | - Lynn E. DeLisi
- Department of Psychiatry, Harvard Medical School, Cambridge Health
Alliance, Cambridge, Massachusetts, USA
| | - Lasse Folkersen
- Institute of Biological Psychiatry, Capital Region Hospitals,
Copenhagen, Denmark
| | - James L. Kennedy
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford,
California, USA
| | - Joseph L. McClay
- Department of Pharmacotherapy and Outcome Science, Virginia
Commonwealth University School of Pharmacy, Richmond, VA, USA
| | - Francis J. McMahon
- Human Genetics Branch, National Institute of Mental Health, Bethesda,
MD, USA
| | - Richard Musil
- Department of Psychiatry and Psychotherapy,
Ludwig-Maximilians-University, Munich, Germany
| | - Nancy L. Saccone
- Departments of Psychiatry and Genetics, Washington University School of
Medicine in St. Louis, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford,
California, USA
| | - Robert M. Stowe
- Departments of Psychiatry and Neurology (Medicine), University of
British Columbia, USA
| | - Ene-Choo Tan
- KK Research Centre, KK Women’s and Children’s Hospital,
Singapore, Singapore
| | - Arun K. Tiwari
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Clement C. Zai
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Gwyneth Zai
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Jianping Zhang
- Department of Psychiatry, Weill Cornell Medical College, New
York-Presbyterian Westchester Division, White Plains, NY, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic
Innovation, Children’s Mercy Kansas City, Kansas City and School of
Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Daniel J Müller
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
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36
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Huddart R, Whirl-Carrillo M, Altman RB, Klein TE. PharmGKB Tutorial for Pharmacogenomics of Drugs Potentially Used in the Context of COVID-19. Clin Pharmacol Ther 2020; 109:116-122. [PMID: 32978778 PMCID: PMC7537078 DOI: 10.1002/cpt.2067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/17/2020] [Indexed: 12/03/2022]
Abstract
Pharmacogenomics (PGx) is a key area of precision medicine, which is already being implemented in some health systems and may help guide clinicians toward effective therapies for individual patients. Over the last 2 decades, the Pharmacogenomics Knowledgebase (PharmGKB) has built a unique repository of PGx knowledge, including annotations of clinical guideline and regulator‐approved drug labels in addition to evidence‐based drug pathways and annotations of the scientific literature. All of this knowledge is freely accessible on the PharmGKB website. In the first of a series of PharmGKB tutorials, we introduce the PharmGKB coronavirus disease 2019 (COVID‐19) portal and, using examples of drugs found in the portal, demonstrate some of the main features of PharmGKB. This paper is intended as a resource to help users become quickly acquainted with the wealth of information stored in PharmGKB.
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Affiliation(s)
- Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
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37
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Lima JJ, Thomas CD, Barbarino J, Desta Z, Van Driest SL, El Rouby N, Johnson JA, Cavallari LH, Shakhnovich V, Thacker DL, Scott SA, Schwab M, Uppugunduri CRS, Formea CM, Franciosi JP, Sangkuhl K, Gaedigk A, Klein TE, Gammal RS, Furuta T. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2C19 and Proton Pump Inhibitor Dosing. Clin Pharmacol Ther 2020; 109:1417-1423. [PMID: 32770672 DOI: 10.1002/cpt.2015] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/27/2022]
Abstract
Proton pump inhibitors (PPIs) are widely used for acid suppression in the treatment and prevention of many conditions, including gastroesophageal reflux disease, gastric and duodenal ulcers, erosive esophagitis, Helicobacter pylori infection, and pathological hypersecretory conditions. Most PPIs are metabolized primarily by cytochrome P450 2C19 (CYP2C19) into inactive metabolites, and CYP2C19 genotype has been linked to PPI exposure, efficacy, and adverse effects. We summarize the evidence from the literature and provide therapeutic recommendations for PPI prescribing based on CYP2C19 genotype (updates at www.cpicpgx.org). The potential benefits of using CYP2C19 genotype data to guide PPI therapy include (i) identifying patients with genotypes predictive of lower plasma exposure and prescribing them a higher dose that will increase the likelihood of efficacy, and (ii) identifying patients on chronic therapy with genotypes predictive of higher plasma exposure and prescribing them a decreased dose to minimize the risk of toxicity that is associated with long-term PPI use, particularly at higher plasma concentrations.
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Affiliation(s)
- John J Lima
- Center for Pharmacogenomics and Translational Research, Nemours Children's Health, Jacksonville, Florida, USA
| | - Cameron D Thomas
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Julia Barbarino
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Zeruesenay Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nihal El Rouby
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Division of Pharmacy Practice & Administrative Sciences, University of Cincinnati James Winkle College of Pharmacy, Cincinnati, Ohio, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Valentina Shakhnovich
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Mercy Kansas City, Kansas City, Missouri, USA.,Center for Children's Healthy Lifestyles & Nutrition, Kansas City, Missouri, USA
| | - David L Thacker
- Department of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Translational Software, Bellevue, Washington, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Chakradhara Rao S Uppugunduri
- CANSEARCH Research Laboratory, Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Oncology-Hematology Unit, Department of Pediatrics, Gynecology, and Obstetrics, Geneva University Hospital, Geneva, Switzerland
| | - Christine M Formea
- Department of Pharmacy Services and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - James P Franciosi
- Division of Gastroenterology, Hepatology, and Nutrition, Nemours Children's Hospital, Orlando, Florida, USA.,Department of Pediatrics, University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA.,Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
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38
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Karnes JH, Rettie AE, Somogyi AA, Huddart R, Fohner AE, Formea CM, Ta Michael Lee M, Llerena A, Whirl-Carrillo M, Klein TE, Phillips EJ, Mintzer S, Gaedigk A, Caudle KE, Callaghan JT. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2C9 and HLA-B Genotypes and Phenytoin Dosing: 2020 Update. Clin Pharmacol Ther 2020; 109:302-309. [PMID: 32779747 DOI: 10.1002/cpt.2008] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
Abstract
Phenytoin is an antiepileptic drug with a narrow therapeutic index and large interpatient pharmacokinetic variability, partly due to genetic variation in CYP2C9. Furthermore, the variant allele HLA-B*15:02 is associated with an increased risk of Stevens-Johnson syndrome and toxic epidermal necrolysis in response to phenytoin treatment. We summarize evidence from the published literature supporting these associations and provide therapeutic recommendations for the use of phenytoin based on CYP2C9 and/or HLA-B genotypes (updates on cpicpgx.org).
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Affiliation(s)
- Jason H Karnes
- Department of Pharmacy Practice & Science, University of Arizona College of Pharmacy, Tucson, Arizona, USA
- Sarver Heart Center, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington School of Pharmacy, Seattle, Washington, USA
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Institute of Public Health Genetics, University of Washington, Seattle, Washington, USA
| | - Christine M Formea
- Department of Pharmacy and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Ming Ta Michael Lee
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Adrian Llerena
- INUBE Extremadura University Biosanitary Research Institute and Medical School, Badajoz, Spain
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine, Stanford University, Stanford, California, USA
| | - Elizabeth J Phillips
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Scott Mintzer
- Department of Neurology, Thomas Jefferson University Hospital Methodist Hospital Division of Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John T Callaghan
- Department of Veteran Affairs and Departments of Medicine and Pharmacology/Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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39
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Huddart R, Gong L, Sangkuhl K, Thorn CF, Whirl-Carrillo M, Caudle KE, Relling MV, Klein TE. Response to: Unveiling the guidance heterogeneity for genome-informed drug treatment interventions among regulatory bodies and research consortia. Pharmacol Res 2020; 158:104838. [DOI: 10.1016/j.phrs.2020.104838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022]
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40
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Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 2020; 109:352-366. [PMID: 32602114 DOI: 10.1002/cpt.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- UNEx, ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA
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41
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Verma SS, Bergmeijer TO, Gong L, Reny JL, Lewis JP, Mitchell BD, Alexopoulos D, Aradi D, Altman RB, Bliden K, Bradford Y, Campo G, Chang K, Cleator JH, Déry JP, Dridi NP, Fernandez-Cadenas I, Fontana P, Gawaz M, Geisler T, Gensini GF, Giusti B, Gurbel PA, Hochholzer W, Holmvang L, Kim EY, Kim HS, Marcucci R, Montaner J, Backman JD, Pakyz RE, Roden DM, Schaeffeler E, Schwab M, Shin JG, Siller-Matula JM, Ten Berg JM, Trenk D, Valgimigli M, Wallace J, Wen MS, Kubo M, Lee MTM, Whaley R, Winter S, Klein TE, Shuldiner AR, Ritchie MD. Genomewide Association Study of Platelet Reactivity and Cardiovascular Response in Patients Treated With Clopidogrel: A Study by the International Clopidogrel Pharmacogenomics Consortium. Clin Pharmacol Ther 2020; 108:1067-1077. [PMID: 32472697 PMCID: PMC7689744 DOI: 10.1002/cpt.1911] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/08/2020] [Indexed: 01/07/2023]
Abstract
Antiplatelet response to clopidogrel shows wide variation, and poor response is correlated with adverse clinical outcomes. CYP2C19 loss‐of‐function alleles play an important role in this response, but account for only a small proportion of variability in response to clopidogrel. An aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify other genetic determinants of clopidogrel pharmacodynamics and clinical response. A genomewide association study (GWAS) was performed using DNA from 2,750 European ancestry individuals, using adenosine diphosphate‐induced platelet reactivity and major cardiovascular and cerebrovascular events as outcome parameters. GWAS for platelet reactivity revealed a strong signal for CYP2C19*2 (P value = 1.67e−33). After correction for CYP2C19*2 no other single‐nucleotide polymorphism reached genomewide significance. GWAS for a combined clinical end point of cardiovascular death, myocardial infarction, or stroke (5.0% event rate), or a combined end point of cardiovascular death or myocardial infarction (4.7% event rate) showed no significant results, although in coronary artery disease, percutaneous coronary intervention, and acute coronary syndrome subgroups, mutations in SCOS5P1, CDC42BPA, and CTRAC1 showed genomewide significance (lowest P values: 1.07e−09, 4.53e−08, and 2.60e−10, respectively). CYP2C19*2 is the strongest genetic determinant of on‐clopidogrel platelet reactivity. We identified three novel associations in clinical outcome subgroups, suggestive for each of these outcomes.
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Affiliation(s)
- Shefali Setia Verma
- Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas O Bergmeijer
- Department of Cardiology, St. Antonius Center for Platelet Function Research, Nieuwegein, The Netherlands
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Jean-Luc Reny
- Internal Medicine, Béziers Hospital, Béziers, France.,Geneva Platelet Group, School of Medicine, University of Geneva, Geneva, Switzerland.,Department of Internal Medicine, Rehabilitation and Geriatrics, University Hospitals of Geneva, Geneva, Switzerland.,Geneva Platelet Group and Division of Angiology and Haemostasis, University Hospitals of Geneva, Geneva, Switzerland
| | - Joshua P Lewis
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Braxton D Mitchell
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, Maryland, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - Dimitrios Alexopoulos
- National and Kapodistrian University of Athens Medical School, Attikon University Hospital, Athens, Greece
| | - Daniel Aradi
- Department of Cardiology, Heart Center Balatonfüred, Balatonfüred, Hungary
| | - Russ B Altman
- Department of Bioengineering, Genetics and Medicine, Stanford University, Stanford, California, USA
| | - Kevin Bliden
- Sinai Center for Thrombosis Research and Drug Development, Baltimore, Maryland, USA
| | - Yuki Bradford
- Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gianluca Campo
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Ferrara and Maria Cecilia Hospital, GVM Care and Research, Cotignola, Italy
| | - Kiyuk Chang
- Department of Internal Medicine, Cardiology Division, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - John H Cleator
- Division of Cardiology and Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean-Pierre Déry
- Quebec Heart and Lung Institute, University Laval, Quebec City, QC, Canada
| | - Nadia P Dridi
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Israel Fernandez-Cadenas
- Neurology, Stroke Pharmacogenomics and Genetics Group, Sant Pau Institute of Research, Barcelona, Spain
| | - Pierre Fontana
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Geneva Platelet Group and Division of Angiology and Haemostasis, University Hospitals of Geneva, Geneva, Switzerland
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University of Tübingen, Tübingen, Germany
| | - Tobias Geisler
- Department of Cardiology and Angiology, Medizinische Klinik III, University Hospital Tübingen, Tübingen, Germany
| | - Gian Franco Gensini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Paul A Gurbel
- Sinai Center for Thrombosis Research and Drug Development, Baltimore, Maryland, USA
| | - Willibald Hochholzer
- Department of Cardiology and Angiology II, University Heart Center Freiburg Bad Krozingen, Bad Krozingen, Germany
| | - Lene Holmvang
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eun-Young Kim
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Busan, South Korea
| | - Ho-Sook Kim
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Busan, South Korea
| | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain
| | - Joshua D Backman
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Ruth E Pakyz
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Dan M Roden
- Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, and Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jae Gook Shin
- Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Busan, South Korea.,Department of Pharmacology and Pharmacogenomics Research Center, Inje University, Busan Paik Hospital, Busan, South Korea
| | - Jolanta M Siller-Matula
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria.,Department of Experimental and Clinical Pharmacology, Centre for Preclinical Research and Technology (CEPT), Medical University of Warsaw, Warsaw, Poland
| | - Jurriën M Ten Berg
- Department of Cardiology, St. Antonius Center for Platelet Function Research, Nieuwegein, The Netherlands
| | - Dietmar Trenk
- Department of Cardiology and Angiology II, University Heart Center Freiburg Bad Krozingen, Bad Krozingen, Germany.,Department of Clinical Pharmacology, University Heart Centre Freiburg, Bad Krozingen, Germany
| | - Marco Valgimigli
- Department of Cardiology, Swiss Cardiovascular Center Bern, Bern University Hospital, Bern, Switzerland
| | - John Wallace
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Ming-Shien Wen
- Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and School of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | | | - Ryan Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Tübingen, Germany
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Alan R Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Marylyn D Ritchie
- Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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42
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Theken KN, Lee CR, Gong L, Caudle KE, Formea CM, Gaedigk A, Klein TE, Agúndez JAG, Grosser T. Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2C9 and Nonsteroidal Anti-Inflammatory Drugs. Clin Pharmacol Ther 2020; 108:191-200. [PMID: 32189324 DOI: 10.1002/cpt.1830] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used analgesics due to their lack of addictive potential. However, NSAIDs have the potential to cause serious gastrointestinal, renal, and cardiovascular adverse events. CYP2C9 polymorphisms influence metabolism and clearance of several drugs in this class, thereby affecting drug exposure and potentially safety. We summarize evidence from the published literature supporting these associations and provide therapeutic recommendations for NSAIDs based on CYP2C9 genotype (updates at www.cpicpgx.org).
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Affiliation(s)
- Katherine N Theken
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Craig R Lee
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Li Gong
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, California, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christine M Formea
- Department of Pharmacy and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Pharmacy and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, California, USA
| | - José A G Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx. ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - Tilo Grosser
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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43
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Gaedigk A, Whirl-Carrillo M, Pratt VM, Miller NA, Klein TE. PharmVar and the Landscape of Pharmacogenetic Resources. Clin Pharmacol Ther 2020; 107:43-46. [PMID: 31758698 PMCID: PMC6925620 DOI: 10.1002/cpt.1654] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | | | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
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44
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Hicks JK, Bishop JR, Gammal RS, Sangkuhl K, Bousman C, Leeder JS, Llerena A, Mueller DJ, Ramsey LB, Scott SA, Skaar TC, Caudle KE, Klein TE, Gaedigk A. A Call for Clear and Consistent Communications Regarding the Role of Pharmacogenetics in Antidepressant Pharmacotherapy. Clin Pharmacol Ther 2020; 107:50-52. [PMID: 31664715 PMCID: PMC6925627 DOI: 10.1002/cpt.1661] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/23/2019] [Indexed: 01/15/2023]
Affiliation(s)
- J. Kevin Hicks
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL, USA
| | - Jeffrey R. Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Roseann S. Gammal
- Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, MA, USA
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Chad Bousman
- Departments of Medical Genetics Psychiatry, Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, Calgary, Alberta, Canada
- Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Adrián Llerena
- CIBERSAM, Madrid, Spain. CICAB Clinical Research Center, Extremadura University Hospital and Medical School, Badajoz, Spain
| | - Daniel J. Mueller
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Ontario, Canada
| | - Laura B. Ramsey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Research in Patient Services and Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Todd C. Skaar
- Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, MO, USA
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45
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Nofziger C, Turner AJ, Sangkuhl K, Whirl-Carrillo M, Agúndez JAG, Black JL, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Gaedigk A. PharmVar GeneFocus: CYP2D6. Clin Pharmacol Ther 2019; 107:154-170. [PMID: 31544239 DOI: 10.1002/cpt.1643] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | - Amy J Turner
- Section of Genomic Pediatrics, Department of Pediatrics, Children's Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Madrid, Spain
| | - John L Black
- Division of Laboratory Genetics and Genomics, Personalized Genomics Laboratory, Mayo Clinic Laboratories, Mayo Clinic, Rochester, Minnesota, USA
| | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanton, Illinois, USA
| | - Gualberto Ruano
- Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, Hartford, Connecticut, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Translational Software, Bellevue, Washington, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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46
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Relling MV, Klein TE, Gammal RS, Whirl-Carrillo M, Hoffman JM, Caudle KE. The Clinical Pharmacogenetics Implementation Consortium: 10 Years Later. Clin Pharmacol Ther 2019; 107:171-175. [PMID: 31562822 DOI: 10.1002/cpt.1651] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/04/2019] [Indexed: 01/07/2023]
Abstract
In 2009, the Clinical Pharmacogenetics Implementation Consortium (CPIC, www.cpicpgx.org), a shared project between Pharmacogenomics Knowledge Base (PharmGKB, http://www.pharmgkb.org) and the National Institutes of Health (NIH), was created to provide freely available, evidence-based, peer-reviewed, and updated pharmacogenetic clinical practice guidelines. To date, CPIC has published 23 guidelines (of which 11 have been updated), covering 19 genes and 46 drugs across several therapeutic areas. CPIC also now provides additional resources to facilitate the implementation of pharmacogenetics into routine clinical practice and the electronic health record. Furthermore, since its inception, CPIC's interactions with other resources, databases, websites, and genomic communities have grown. The purpose of this paper is to highlight the progress of CPIC over the past 10 years.
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Affiliation(s)
- Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA
| | | | - James M Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Office of Quality & Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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47
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Caudle KE, Sangkuhl K, Whirl-Carrillo M, Swen JJ, Haidar CE, Klein TE, Gammal RS, Relling MV, Scott SA, Hertz DL, Guchelaar HJ, Gaedigk A. Standardizing CYP2D6 Genotype to Phenotype Translation: Consensus Recommendations from the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group. Clin Transl Sci 2019; 13:116-124. [PMID: 31647186 PMCID: PMC6951851 DOI: 10.1111/cts.12692] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
Translating CYP2D6 genotype to metabolizer phenotype is not standardized across clinical laboratories offering pharmacogenetic (PGx) testing and PGx clinical practice guidelines, such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). The genotype to phenotype translation discordance between laboratories and guidelines can cause discordant cytochrome P450 2D6 (CYP2D6) phenotype assignments and, thus lead to inconsistent therapeutic recommendations and confusion among patients and clinicians. A modified-Delphi method was used to obtain consensus for a uniform system for translating CYP2D6 genotype to phenotype among a panel of international CYP2D6 experts. Experts with diverse involvement in CYP2D6 interpretation (clinicians, researchers, genetic testing laboratorians, and PGx implementers; n = 37) participated in conference calls and surveys. After completion of 7 surveys, a consensus (> 70%) was reached with 82% of the CYP2D6 experts agreeing to the final CYP2D6 genotype to phenotype translation method. Broad adoption of the proposed CYP2D6 genotype to phenotype translation method by guideline developers, such as CPIC and DPWG, and clinical laboratories as well as researchers will result in more consistent interpretation of CYP2D6 genotype.
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Affiliation(s)
- Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Cyrine E Haidar
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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48
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Thorn CF, Whirl-Carrillo M, Hachad H, Johnson JA, McDonagh EM, Ratain MJ, Relling MV, Scott SA, Altman RB, Klein TE. Essential Characteristics of Pharmacogenomics Study Publications. Clin Pharmacol Ther 2019; 105:86-91. [PMID: 30406943 DOI: 10.1002/cpt.1279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022]
Abstract
Pharmacogenomics (PGx) can be seen as a model for biomedical studies: it includes all disease areas of interest and spans in vitro studies to clinical trials, while focusing on the relationships between genes and drugs and the resulting phenotypes. This review will examine different characteristics of PGx study publications and provide examples of excellence in framing PGx questions and reporting their resulting data in a way that maximizes the knowledge that can be built on them.
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Affiliation(s)
- Caroline F Thorn
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
| | | | - Houda Hachad
- Translational Software, Bellevue, Washington, USA
| | - Julie A Johnson
- College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | | | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Mary V Relling
- Pharmaceutical Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Russ B Altman
- Department of Genetics, Department of Computer Science, Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
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49
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Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2019; 107:203-210. [PMID: 31306493 PMCID: PMC6977333 DOI: 10.1002/cpt.1568] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/11/2019] [Indexed: 11/07/2022]
Abstract
Pharmacogenomics (PGx) decision support and return of results is an active area of precision medicine. One challenge of implementing PGx is extracting genomic variants and assigning haplotypes in order to apply prescribing recommendations and information from the Clinical Pharmacogenetics Implementation Consortium (CPIC), the US Food and Drug Administration (FDA), the Pharmacogenomics Knowledgebase (PharmGKB), etc. Pharmacogenomics Clinical Annotation Tool (PharmCAT) (i) extracts variants specified in guidelines from a genetic data set derived from sequencing or genotyping technologies, (ii) infers haplotypes and diplotypes, and (iii) generates a report containing genotype/diplotype-based annotations and guideline recommendations. We describe PharmCAT and a pilot validation project comparing results for 1000 Genomes Project sequences of Coriell samples with corresponding Genetic Testing Reference Materials Coordination Program (GeT-RM) sample characterization. PharmCAT was highly concordant with the GeT-RM data. PharmCAT is available in GitHub to evaluate, test, and report results back to the community. As precision medicine becomes more prevalent, our ability to consistently, accurately, and clearly define and report PGx annotations and prescribing recommendations is critical.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | | | - Ryan M Whaley
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Adam Lavertu
- Biomedical Informatics Training Program, Stanford University, Palo Alto, California, USA
| | - Russ B Altman
- Departments of Biomedical Data Science, Biomedical Engineering, Genetics and Medicine, Stanford University, Palo Alto, California, USA
| | - Lester Carter
- formerly Department of Genetics, Stanford University, Palo Alto, California, USA
| | - Anurag Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Palo Alto, California, USA
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50
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Desta Z, Gammal RS, Gong L, Whirl-Carrillo M, Gaur AH, Sukasem C, Hockings J, Myers A, Swart M, Tyndale RF, Masimirembwa C, Iwuchukwu OF, Chirwa S, Lennox J, Gaedigk A, Klein TE, Haas DW. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2B6 and Efavirenz-Containing Antiretroviral Therapy. Clin Pharmacol Ther 2019; 106:726-733. [PMID: 31006110 DOI: 10.1002/cpt.1477] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/12/2019] [Indexed: 01/11/2023]
Abstract
The HIV type-1 nonnucleoside reverse transcriptase inhibitor, efavirenz, is widely used to treat HIV type-1 infection. Efavirenz is predominantly metabolized into inactive metabolites by cytochrome P450 (CYP)2B6, and patients with certain CYP2B6 genetic variants may be at increased risk for adverse effects, particularly central nervous system toxicity and treatment discontinuation. We summarize the evidence from the literature and provide therapeutic recommendations for efavirenz prescribing based on CYP2B6 genotypes.
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Affiliation(s)
- Zeruesenay Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Roseann S Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences University School of Pharmacy, Boston, Massachusetts, USA.,Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Aditya H Gaur
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Faculty of Medicine Ramathibodi Hospital, Department of Pathology, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Faculty of Medicine Ramathibodi Hospital, Somdech Phra Debaratana Medical Center, Bangkok, Thailand
| | - Jennifer Hockings
- Department of Pharmacy and Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alan Myers
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Sciences Center School of Dentistry, Houston, Texas, USA
| | - Marelize Swart
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rachel F Tyndale
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Collen Masimirembwa
- African Institute of Biomedical Science & Technology, Wilkins Hospital, Harare, Zimbabwe
| | - Otito F Iwuchukwu
- Division of Pharmaceutical Sciences, Fairleigh Dickinson University School of Pharmacy, Florham Park, New Jersey, USA
| | - Sanika Chirwa
- Department of Internal Medicine, Meharry Medical College School of Medicine, Nashville, Tennessee, USA
| | - Jeffrey Lennox
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - David W Haas
- Department of Internal Medicine, Meharry Medical College School of Medicine, Nashville, Tennessee, USA.,Departments of Medicine, Pharmacology, Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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